Edit: I see your link points to your thread at D9. Sorry. (I remember the thread now).
Seems your mail did not get through (maybe post the INI in your thread at Doom9 as an attachment or just as a quote).
BTW: This actually happened to me when re-authoring a menu I had made. The SPU did not display at all, even though it was definitely there (no visual glitch though).
Anyway, to answer your question, have you tried, demuxing after editing and remuxing with muxman (a bad mux is often the issue with this sorta stuff)? Or converting the subbies to SRT and using Subtitle Creator?